Light Microscopy core for NIDDK

National Institute Of Diabetes And Digestive And Kidney Diseases

Investigators

Abstract

The mission of the National Institutes of Health (NIH) is to seek fundamental knowledge about the nature and behavior of living systems and to apply that knowledge to enhance health, lengthen life, and reduce illness and disability. As part of the NIH, the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) Intramural Research Program (IRP) conducts biomedical research and training related to diabetes mellitus; endocrine, bone, and metabolic diseases; digestive diseases, including liver diseases and nutritional disorders; and kidney, urologic, and hematologic diseases. Intramural research is conducted in the Institute's laboratories and clinical facilities in Bethesda, Maryland and in Phoenix, Arizona. There are currently 17 Laboratories and Branches (i.e. 17 departments with different focus areas) in the NIDDK IRP. Most if not all of these areas of research, either occasionally or on an ongoing basis, require light microscopy (LM) methods to qualitatively complement other assays, or as the basis of a quantitative assay. There are three main categories of LM. Conventional widefield, transmitted light techniques, such as darkfield or differential interference contrast (DIC), are still useful because of their innate ability to show cellular morphology. Second, an old standby, immunohistochemistry (IHC)-- using absorptive probes to colorize tissue in transmitted light-- has been used for decades (e.g. in pathology), but recent advances with new probes and color deconvolution have allowed the field to grow, although requiring more finesse when being quantitated. The third and most common category of LM is characterized by the use of fluorescent probes targeting biomolecules (specific proteins, DNA, etc) of interest, making them glow with different colors on a black background. Such fluorescent dyes can even be used to monitor subcellular events in real-time. There are many sub-categories of fluorescence microscopy, e.g. confocal, super-resolution, and TIRF (Total Internal Reflectance-induced Fluorescence). Each of these involve specialized technique in sample prep, image acquisition, and/or image analysis. Some NIDDK labs might be comfortable without advanced help on one of more of the techniques described above, and might also be able to set aside a budget for equipment they would use regularly; but to fill any gaps, the NIDDK Advanced Light Microscopy & Image Analysis Core (ALMIAC) remains a reliable resource for cutting-edge light microscopy equipment, software, and expertise. For the FY2021 budget year (October 2021 - September 2022), there were >50 researchers using ALMIAC resources, representing >28 (out of 96) "Sections" (individual labs), from at least 13 (out of 17) Laboratories and Branches. In other words, 75% of NIDDK labs/branches used ALMIAC resources. Out of the 50+ individual researchers helped, there were at least 9 NIDDK publications during FY 2022 that used images acquired and/or analyzed with the help of ALMIAC resources: --Temesgen E Andargie, Naoko Tsuji, Fayaz Seifuddin, Moon Kyoo Jang, Peter St Yuen, Hyesik Kong, Ilker Tunc, Komudi Singh, Ananth Charya, Kenneth Wilkins, Steven Nathan, Andrea Cox, Mehdi Pirooznia, Robert A Star, Sean Agbor-Enoh. Cell-free DNA maps COVID-19 tissue injury and risk of death and can cause tissue injury. JCI Insight. 2021 Apr 8;6(7):e147610. PMID:33651717 PMCID:PMC8119224 DOI:10.1172/jci.insight.147610. --Daniel Chauss, Tilo Freiwald, Reuben McGregor, Bingyu Yan, Luopin Wang, Estefania Nova-Lamperti, Dhaneshwar Kumar, Zonghao Zhang, Heather Teague, Erin E West, Kevin M Vannella, Marcos J Ramos-Benitez, Jack Bibby, Audrey Kelly, Amna Malik, Alexandra F Freeman, Daniella M Schwartz, Didier Portilla, Daniel S Chertow, Susan John, Paul Lavender, Claudia Kemper, Giovanna Lombardi, Nehal N Mehta, Nichola Cooper, Michail S Lionakis, Arian Laurence, Majid Kazemian, Behdad Afzali. Autocrine vitamin D signaling switches off pro-inflammatory programs of TH 1 cells. Nat Immunol. 2022 Jan;23(1):62-74. doi: 10.1038/s41590-021-01080-3. PMID:34764490 PMCID:PMC7612139 DOI:10.1038/s41590-021-01080-3. --Shue Chen, Leah F Rosin, Gianluca Pegoraro, Nellie Moshkovich, Patrick J Murphy, Guoyun Yu, Elissa P Lei. NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization. Nucleic Acids Res. 2022 Aug 12;50(14):7906-7924. PMID:35819192 PMCID:PMC9371915 DOI:10.1093/nar/gkac600. --Moriah Eustice, Jeff M. Reece, Daniel Konzman, Salil Ghosh, Jhullian Alston, Tyler Hansen, Andy Golden, Michelle R. Bond, John A. Hanover. Nutrient sensing pathways regulating adult reproductive diapause in C. elegans. PLOS one. In Press (2022). --Peng Gao, Miao Xu, Qi Zhang, Catherine Z Chen, Hui Guo, Yihong Ye, Wei Zheng, and Min Shen. Graph Convolutional Network-Based Screening Strategy for Rapid Identification of SARS-CoV-2 Cell-Entry Inhibitors. J Chem Inf Model. 2022 Apr 25; 62(8): 19881997. PMID:35404596 PMCID:PMC9016773 DOI:10.1021/acs.jcim.2c00222. --Juhyung Lee, Yue Xu, Layla Saidi, Miao Xu, Konrad Zinsmaier, Yihong Ye. Abnormal triaging of misfolded proteins by adult neuronal ceroid lipofuscinosis-associated DNAJC5/CSP mutants causes lipofuscin accumulation. Autophagy. 2022 May 4;1-20. PMID:35506243 DOI:10.1080/15548627.2022.2065618. --Qingcai Meng, Daniel Stoyko, Celine Marlin Andrews, Parthena Konstantinidou, Pavol Genzor, Timothy O, Alexandra R Elchert, Leif Benner, Sushil Sobti, Esther Y Katz, Astrid D Haase. Functional editing of endogenous genes through rapid selection of cell pools (Rapid generation of endogenously tagged genes in Drosophila ovarian somatic sheath cells). Nucleic Acids Res. 2022 Aug 26;50(15):e90. PMID:35639929 PMCID:PMC9410888 DOI:10.1093/nar/gkac448. --Leah F Rosin, Dahong Chen, Yang Chen, Elissa P Lei. Dosage compensation in Bombyx mori is achieved by partial repression of both Z chromosomes in males. Proc Natl Acad Sci USA. 2022 Mar b;119(10):e2113374119. PMID:35239439 PMCID:PMC8915793 DOI:10.1073/pnas.2113374119 --Qi Zhang, Peter Radvak, Juhyung Lee, Yue Xu, Vivian Cao-Dao, Miao Xu, Wei Zheng, Catherine Z. Chen, Hang Xie & Yihong Ye. Mitoxantrone modulates a heparan sulfate-spike complex to inhibit SARS-CoV-2 infection. Sci Rep 12, 6294 (2022). PMID:35440680 PMCID:PMC9016215 DOI:10.1038/s41598-022-10293-x. In addition to the specific research projects mentioned above, several areas of improvement in capability and workflow include: 1) Continued deployment of new spinning disk confocal microscope with super-resolution capability, the Nikon CSU-W1 SoRa, which has become the most popular microscope in the ALMIAC. 2) Upgrades to several ALMIAC microscopes, and helping with upgrades to NIDDK microscopes outside the ALMIAC. 3) Conversion of the Huygens deconvolution software to a floating license, available to any NIDDK computer on the internet. 4) With the help of NIDDK CTB (Computer Technology Branch), continued work on the beta version of the NIDDK ALMIAC website. 5) Reorganization of the ALMIAC Director's office and one of the microscope rooms, after a flood forced everything to be moved out.